TB-Profiler result

Run: SRR1169157
Summary

Run ID: SRR1169157

Sample name:

Date: 03-04-2023 02:47:55

Number of reads: 1134445

Percentage reads mapped: 97.99

Strain: lineage4.3.4.2.1

Drug-resistance: MDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rpoB 761140 p.His445Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575538 p.Asp64Gly missense_variant 1.0
rpoC 764744 p.Arg459Trp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765494 p.Val709Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779050 p.Glu21Lys missense_variant 0.25
mmpR5 779455 p.Arg156* stop_gained 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167872 p.Ser914* stop_gained 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715366 c.-34C>G upstream_gene_variant 0.11
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568574 p.Leu36Ile missense_variant 0.11
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiB 3641893 p.Leu120Pro missense_variant 0.12
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3878489 p.Pro7Thr missense_variant 0.1
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244906 c.1674C>T synonymous_variant 0.1
ethA 4326853 c.612_620dupGCTGCAGCG disruptive_inframe_insertion 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407714 p.Lys163Asn missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0